Make notebook transformations identical to CLI (#61)

* Obvious additions after run-through

* Make notebook transformations identical to CLI

Author: dwhswenson

rbfe_tutorial/python_tutorial.ipynb

@@ -44,9 +44,7 @@
    "source": [
     "from rdkit import Chem\n",
     "supp = Chem.SDMolSupplier(\"tyk2_ligands.sdf\", removeHs=False)\n",
-    "ligands = [openfe.SmallMoleculeComponent.from_rdkit(mol) for mol in supp]\n",
-    "\n",
-    "name_to_ligand = {ligand.name: ligand for ligand in ligands}"
+    "ligands = [openfe.SmallMoleculeComponent.from_rdkit(mol) for mol in supp]"
    ]
   },
   {
@@ -173,7 +171,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 7,
    "id": "2263838f",
    "metadata": {},
    "outputs": [],
@@ -212,7 +210,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 8,
    "id": "9d2fbc22",
    "metadata": {},
    "outputs": [],
@@ -223,7 +221,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 9,
    "id": "3f1706ee",
    "metadata": {},
    "outputs": [],
@@ -233,7 +231,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 10,
    "id": "710285ca",
    "metadata": {},
    "outputs": [],
@@ -262,7 +260,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 11,
    "id": "3f394a0d",
    "metadata": {
     "scrolled": true
@@ -282,7 +280,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 12,
    "id": "fb839094",
    "metadata": {},
    "outputs": [
@@ -298,7 +296,7 @@
        "298.15 <Unit('kelvin')>"
       ]
      },
-     "execution_count": 13,
+     "execution_count": 12,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -310,7 +308,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 13,
    "id": "e83630f0",
    "metadata": {},
    "outputs": [],
@@ -331,7 +329,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 14,
    "id": "7adf42d6",
    "metadata": {},
    "outputs": [],
@@ -352,7 +350,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 15,
    "id": "44ba94ca",
    "metadata": {},
    "outputs": [],
@@ -388,7 +386,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 16,
    "id": "66666a80",
    "metadata": {},
    "outputs": [],
@@ -410,12 +408,14 @@
     "        sysA = openfe.ChemicalSystem(sysA_dict, name=f\"{mapping.componentA.name}_{leg}\")\n",
     "        sysB = openfe.ChemicalSystem(sysB_dict, name=f\"{mapping.componentB.name}_{leg}\")\n",
     "        \n",
+    "        prefix = \"easy_rbfe_\"  # prefix is only to exactly reproduce CLI\n",
+    "        \n",
     "        transformation = openfe.Transformation(\n",
     "            stateA=sysA,\n",
     "            stateB=sysB,\n",
     "            mapping={'ligand': mapping},\n",
     "            protocol=protocol,  # use protocol created above\n",
-    "            name=f\"{sysA.name}_{sysB.name}\"\n",
+    "            name=f\"{prefix}{sysA.name}_{sysB.name}\"\n",
     "        )\n",
     "        transformations.append(transformation)\n",
     "\n",
@@ -434,7 +434,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 17,
    "id": "d6cebd9a",
    "metadata": {},
    "outputs": [],
@@ -451,32 +451,32 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 18,
    "id": "b96b57a9",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "lig_ejm_31_complex_lig_ejm_42_complex.json\r\n",
-      "lig_ejm_31_complex_lig_ejm_46_complex.json\r\n",
-      "lig_ejm_31_complex_lig_ejm_47_complex.json\r\n",
-      "lig_ejm_31_complex_lig_ejm_48_complex.json\r\n",
-      "lig_ejm_31_complex_lig_ejm_50_complex.json\r\n",
-      "lig_ejm_31_solvent_lig_ejm_42_solvent.json\r\n",
-      "lig_ejm_31_solvent_lig_ejm_46_solvent.json\r\n",
-      "lig_ejm_31_solvent_lig_ejm_47_solvent.json\r\n",
-      "lig_ejm_31_solvent_lig_ejm_48_solvent.json\r\n",
-      "lig_ejm_31_solvent_lig_ejm_50_solvent.json\r\n",
-      "lig_ejm_42_complex_lig_ejm_43_complex.json\r\n",
-      "lig_ejm_42_solvent_lig_ejm_43_solvent.json\r\n",
-      "lig_ejm_46_complex_lig_jmc_23_complex.json\r\n",
-      "lig_ejm_46_complex_lig_jmc_27_complex.json\r\n",
-      "lig_ejm_46_complex_lig_jmc_28_complex.json\r\n",
-      "lig_ejm_46_solvent_lig_jmc_23_solvent.json\r\n",
-      "lig_ejm_46_solvent_lig_jmc_27_solvent.json\r\n",
-      "lig_ejm_46_solvent_lig_jmc_28_solvent.json\r\n"
+      "easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json\r\n",
+      "easy_rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json\r\n",
+      "easy_rbfe_lig_ejm_31_complex_lig_ejm_47_complex.json\r\n",
+      "easy_rbfe_lig_ejm_31_complex_lig_ejm_48_complex.json\r\n",
+      "easy_rbfe_lig_ejm_31_complex_lig_ejm_50_complex.json\r\n",
+      "easy_rbfe_lig_ejm_31_solvent_lig_ejm_42_solvent.json\r\n",
+      "easy_rbfe_lig_ejm_31_solvent_lig_ejm_46_solvent.json\r\n",
+      "easy_rbfe_lig_ejm_31_solvent_lig_ejm_47_solvent.json\r\n",
+      "easy_rbfe_lig_ejm_31_solvent_lig_ejm_48_solvent.json\r\n",
+      "easy_rbfe_lig_ejm_31_solvent_lig_ejm_50_solvent.json\r\n",
+      "easy_rbfe_lig_ejm_42_complex_lig_ejm_43_complex.json\r\n",
+      "easy_rbfe_lig_ejm_42_solvent_lig_ejm_43_solvent.json\r\n",
+      "easy_rbfe_lig_ejm_46_complex_lig_jmc_23_complex.json\r\n",
+      "easy_rbfe_lig_ejm_46_complex_lig_jmc_27_complex.json\r\n",
+      "easy_rbfe_lig_ejm_46_complex_lig_jmc_28_complex.json\r\n",
+      "easy_rbfe_lig_ejm_46_solvent_lig_jmc_23_solvent.json\r\n",
+      "easy_rbfe_lig_ejm_46_solvent_lig_jmc_27_solvent.json\r\n",
+      "easy_rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent.json\r\n"
      ]
     }
    ],